Preparation and Analysis of an Expressed Sequence Tag Library from the Toxic Dinoflagellate Alexandrium catenella

Uribe, Paulina; Fuentes, Daniela; Valdés, Jorge Hernández; Shmaryahu, Amir; Zúñiga, Alicia; Holmes, David S.; Valenzuela, Pablo

doi:10.1007/s10126-008-9107-8

Cited by 44 publications

(48 citation statements)

References 44 publications

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“…For instance, in a K. brevis cDNA library (13), 4,399 of the total of 5,280 cDNA clusters contained single ESTs, 881 contained 2-31 ESTs, and the 24 most highly expressed gene clusters were each represented by 10-50 ESTs. In an A. catenella cDNA library (15), the sequenced 9,847 ESTs contained 6,496 unigene clusters, with the majority Bootstrap support of nodes leading to dinoflagellate-containing clades (arrow) was from maximum likelihood analysis. Taxa are shown by abbreviated species names followed by GenBank accession numbers.…”

Section: Discussionmentioning

confidence: 99%

Spliced leader–based metatranscriptomic analyses lead to recognition of hidden genomic features in dinoflagellates

Lin

Zhang

Zhuang

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

163

139

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Environmental transcriptomics (metatranscriptomics) for a specific lineage of eukaryotic microbes (e.g., Dinoflagellata) would be instrumental for unraveling the genetic mechanisms by which these microbes respond to the natural environment, but it has not been exploited because of technical difficulties. Using the recently discovered dinoflagellate mRNA-specific spliced leader as a selective primer, we constructed cDNA libraries (e-cDNAs) from one marine and two freshwater plankton assemblages. Small-scale sequencing of the e-cDNAs revealed functionally diverse transcriptomes proven to be of dinoflagellate origin. A set of dinoflagellate common genes and transcripts of dominant dinoflagellate species were identified. Further analyses of the dataset prompted us to delve into the existing, largely unannotated dinoflagellate EST datasets (DinoEST). Consequently, all four nucleosome core histones, two histone modification proteins, and a nucleosome assembly protein were detected, clearly indicating the presence of nucleosome-like machinery long thought not to exist in dinoflagellates. The isolation of rhodopsin from taxonomically and ecotypically diverse dinoflagellates and its structural similarity and phylogenetic affinity to xanthorhodopsin suggest a common genetic potential in dinoflagellates to use solar energy nonphotosynthetically. Furthermore, we found 55 cytoplasmic ribosomal proteins (RPs) from the e-cDNAs and 24 more from DinoEST, showing that the dinoflagellate phylum possesses all 79 eukaryotic RPs. Our results suggest that a sophisticated eukaryotic molecular machine operates in dinoflagellates that likely encodes many more unsuspected physiological capabilities and, meanwhile, demonstrate that unique spliced leaders are useful for profiling lineage-specific microbial transcriptomes in situ.metatranscriptome | eukaryote | gene expression | alveolate

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Section: Discussionmentioning

confidence: 99%

Spliced leader–based metatranscriptomic analyses lead to recognition of hidden genomic features in dinoflagellates

Lin

Zhang

Zhuang

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

163

139

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“…Two different parts of this saxitoxin gene cluster were found to be somewhat similar to two dinoflagellate ESTs, one from an A. catenella library and one from A. tamarense (Moustafa et al, 2009). At the time of the study by Moustafa et al (2009), several large-scale sequence databases for PST-producing Alexandrium species were available (Hackett et al, 2005;Erdner & Anderson, 2006;Uribe et al, 2008), so the sparseness of identified similarities might be due to a considerable change in the sxt genes after their HGT to dinoflagellates. During the long evolutionary timescale the sxt genes might have changed beyond recognition.…”

Section: Aphanizomenon Flos-aqua)mentioning

confidence: 98%

Grazer-induced toxin formation in dinoflagellates: a transcriptomic model study

Yang

Selander

Pavia

et al. 2011

European Journal of Phycology

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The cosmopolitan marine dinoflagellate Alexandrium minutum is known to produce toxins causing paralytic shellfish poisoning (PSP). As has recently been shown, this toxicity can be enhanced by the presence of certain copepod species. Inducible defences are known from a variety of marine organisms, but the associated transcriptomic changes have only been investigated in model angiosperms. Here, we use a microarray approach to investigate the changes in gene expression during the copepodprovoked induction of higher toxicity in A. minutum. We found a limited set of 14 genes (0.35% of the tested sequences) to be affected by copepod presence; gene expression changed by a factor of 1.9 to 11.4 when compared with control samples. We compared the differentially expressed genes after one day -before the onset of augmented toxicity -and after 3 days, when cellular toxin content in the induced samples was five times higher than in control cultures. Comparison with differences previously found between toxic and non-toxic strains revealed two sequences apparently associated with PSP toxin content. Our study is the first investigation of transcriptomic effects associated with grazer-induced induction of elevated toxicity in a protist. This provides a novel approach to the ecology of predator-prey interactions, as well as a highly targeted method for investigating the genes associated with toxin production and regulation in toxic dinoflagellates.

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“…Light is produced intracellularly in organelles called scintillons [10]. These contain the enzyme luciferase and a luciferin substrate, which in some species is stabilised by a luciferin binding protein [11]–[13]. When cells are mechanically agitated, the luminescent chemistry is activated producing blue light in the form of brief and bright flashes (reviewed by [14]).…”

Section: Introductionmentioning

confidence: 99%

Molecular Detection of Bioluminescent Dinoflagellates in Surface Waters of the Patagonian Shelf during Early Austral Summer 2008

et al. 2014

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We investigated the distribution of bioluminescent dinoflagellates in the Patagonian Shelf region using “universal” PCR primers for the dinoflagellate luciferase gene. Luciferase gene sequences and single cell PCR tests, in conjunction with taxonomic identification by microscopy, allowed us to identify and quantify bioluminescent dinoflagellates. We compared these data to coincidental discrete optical measurements of stimulable bioluminescence intensity. Molecular detection of the luciferase gene showed that bioluminescent dinoflagellates were widespread across the majority of the Patagonian Shelf region. Their presence was comparatively underestimated by optical bioluminescence measurements, whose magnitude was affected by interspecific differences in bioluminescence intensity and by the presence of other bioluminescent organisms. Molecular and microscopy data showed that the complex hydrography of the area played an important role in determining the distribution and composition of dinoflagellate populations. Dinoflagellates were absent south of the Falkland Islands where the cold, nutrient-rich, and well-mixed waters of the Falklands Current favoured diatoms instead. Diverse populations of dinoflagellates were present in the warmer, more stratified waters of the Patagonian Shelf and Falklands Current as it warmed northwards. Here, the dinoflagellate population composition could be related to distinct water masses. Our results provide new insight into the prevalence of bioluminescent dinoflagellates in Patagonian Shelf waters and demonstrate that a molecular approach to the detection of bioluminescent dinoflagellates in natural waters is a promising tool for ecological studies of these organisms.

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Preparation and Analysis of an Expressed Sequence Tag Library from the Toxic Dinoflagellate Alexandrium catenella

Cited by 44 publications

References 44 publications

Spliced leader–based metatranscriptomic analyses lead to recognition of hidden genomic features in dinoflagellates

Spliced leader–based metatranscriptomic analyses lead to recognition of hidden genomic features in dinoflagellates

Grazer-induced toxin formation in dinoflagellates: a transcriptomic model study

Molecular Detection of Bioluminescent Dinoflagellates in Surface Waters of the Patagonian Shelf during Early Austral Summer 2008

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